Blender is not rendering my animation in Cycles, even though it is set to that, why?
If there are image strips in the Video Sequencer editor, Blender ignores the scene and the cameras, rendering the image strip instead. Deleting the image strip or unchecking the "Sequencer" checkbox should solve your issue.



Generally, however, I'd recommend that you process the image strips in a different file from the one you used for rendering.